In 1824 Thomas M. Duke explored the area and reported to Stephen F. Austin, describing the Waco village:

"This town is situated on the West Bank of the River. They have a spring almost as cold as ice itself. All we want is some Brandy and Sugar to have Ice Toddy. They have about planted in corn, beans, pumpkins, and melons and that tended in good order. I think they cannot raise more than One Hundred Warriors."

After Austin aborted the first attempt to destroy their village in 1825, he made a treaty with them. The Waco eventually moved out of the region, settling north near present-day Fort Worth. In 1872 they joined other Wichita tribes on a reservation in Oklahoma. In 1902 the Waco received allotments of land and became official US citizens.

Neil McLennan settled in an area near the South Bosque River in 1838. Jacob De Cordova bought McLennan's property and hired a former Texas Ranger and surveyor named George B. Erath to inspect the area. In 1849, Erath designed the first block of the city. Property owners wanted to name the city Lamartine, but Erath convinced them to name the area Waco Village, in honor of the Native Americans who had lived there. In March 1849, Shapley Ross built the first house in Waco, a double-log cabin, on a bluff overlooking the springs. His daughter Kate was the first white child to be born in Waco.

1866–1900

In 1866, Waco's leading citizens embarked on an ambitious project to build the first bridge to span the wide Brazos River. They formed the Waco Bridge Company to build the brick Waco Suspension Bridge, which was completed in 1870. The company commissioned a firm owned by John Augustus Roebling in Trenton, New Jersey, to supply the cables and steelwork for the bridge, and contracted with Mr. Thomas M. Griffith, a civil engineer based in New York, for the supervisory engineering work on the bridge. The economic effects of the Waco bridge were immediate and large. The cowboys and cattle-herds following the Chisholm Trail north, crossed the Brazos River at Waco. Some chose to pay the Suspension Bridge toll, while others floated their herds down the river. The population of Waco grew rapidly, as immigrants now had a safe crossing for their horse-drawn carriages and wagons. Since 1971, the bridge has been open only to pedestrian traffic and is in the National Register of Historic Places.

In the late 19th century a red-light district called the "Reservation" grew up in Waco, and prostitution was regulated by the city. The Reservation was suppressed in the early 20th century. In 1885, the soft drinkDr Pepper was invented in Waco at Morrison's Old Corner Drug Store.

In 1845, Baylor University was founded in Independence, Texas, making it the oldest institution of higher learning in the state of Texas. It moved to Waco in 1886 and merged with Waco University, becoming an integral part of the city. The university's Strecker Museum was also the oldest continuously operating museum in the state until it closed in 2003, and the collections were moved to the new Mayborn Museum Complex. In 1873, AddRan College was founded by brothers Addison and Randolph Clark in Fort Worth. The school moved to Waco in 1895, changing its name to Add-Ran Christian University and taking up residence in the empty buildings of Waco Female College. Add-Ran changed its name to Texas Christian University in 1902 and left Waco after the school's main building burned down in 1910. TCU was offered a campus and $200,000 by the city of Fort Worth to relocate there.

In the 1890s, William Cowper Brann published the highly successful Iconoclast newspaper in Waco. One of his targets was Baylor University. Brann revealed that Baylor officials had been importing South American children recruited by missionaries and making house-servants out of them. Brann was shot in the back by Tom Davis, a Baylor supporter. Brann then wheeled, drew his pistol, and killed Davis. Brann was helped home by his friends, and died there of his wounds.

In 1894, the first Cotton Palace fair and exhibition center was built to reflect the dominant contribution of the agricultural cotton industry in the region. Since the end of the Civil War, cotton had been cultivated in the Brazos and Bosque valleys, and Waco had become known nationwide as a top producer. Over the next 23 years, the annual exposition would welcome over eight million attendees. The opulent building which housed the month-long exhibition was destroyed by fire and rebuilt in 1910. In 1931, the exposition fell prey to the Great Depression, and the building was torn down. However, the annual Cotton Palace Pageant continues, hosted in late April in conjunction with the Brazos River Festival.

On September 15, 1896, "The Crash" took place about north of Waco. "The Crash at Crush" was a publicity stunt done by the Missouri–Kansas–Texas Railroad company (known as M-K-T or "Katy"), featuring two locomotives intentionally set to a head-on collision. Meant to be a family fun event with food, games and entertainment, the Crash turned deadly when both boilers exploded simultaneously, sending metal flying in the air. Two people died and six were seriously injured.

1901–present

Built in 1902 Waco Steel Bridge was the longest single span steel bridge in the world.

In 1916, an African American teenager named Jesse Washington was tortured, mutilated and burned to death in the town square by a mob that seized him from the courthouse, where he had been convicted of murdering a white woman. 15,000 spectators, mostly citizens of Waco, were present. The commonly-named Waco Horror drew international condemnation and became the cause célèbre of the nascent NAACP's anti-lynching campaign. In 2006, the Waco City Council officially condemned the lynching, which took place without opposition from local political or judicial leaders.

In the 1920s, despite the popularity of the Ku Klux Klan and high numbers of lynchings throughout Texas, Waco's authorities attempted to respond to the NAACP's campaign and institute more protections for African-Americans or others threatened with mob violence and lynching. In 1923, Waco's Sheriff Leslie Stegall protected Roy Mitchell, an African American coerced into confessing to multiple murders, from mob lynching. Mitchell was the last Texan to be publicly executed in Texas, and also the last to be hanged before the introduction of the electric chair.[1] In the same year the Texas Legislature created the Tenth Civil Court of Appeals and placed it in Waco; it is now known as the 10th Court of Appeals.

In 1937, Grover C. Thomsen and R.H. Roark created a soft-drink called "Sun Tang Red Cream Soda". This would later become known as the soft drink Big Red.

On May 11, 1953, a tornado hit downtown Waco, killing 114. As of 2011, it remains the eleventh deadliest tornado in U.S. history and tied for the deadliest in Texas state history.[2] It was the first tornado tracked by radar and helped spur the creation of a nationwide storm surveillance system. A 2.5 ton granite monument, featuring the names of those killed, was placed downtown in 2004.

In 1964 the Texas Department of Public Safety designated Waco as the site for the state-designated official museum of the legendary Texas Rangers law enforcement agency founded in 1823. In 1976 it was further designated the official Hall of Fame for the Rangers and renamed the Texas Ranger Hall of Fame and Museum. Renovations by the Waco government earned this building green status, the first Waco government-led project of its nature. The construction project has fallen under scrutiny for expanding the building over unmarked human graves.

In 1978, bones were discovered emerging from the mud at the confluence of the Brazos River and the Bosque River. Subsequent excavations revealed that the bones were 68,000 years old and belonged to a species of mammoth. Eventually, the remains of at least 24 mammoths, one camel, and one large cat were found at the site, making it one of the largest findings of its kind. Scholars have puzzled over why such a large herd had been killed all at once. The site is currently being looked at by the National Park Service for possible inclusion into the National Park system. They are conducting a special resource study to be presented to Congress.
The bones are currently on display at the Waco Mammoth Site.

In 1999, a charter school called the Emma L. Harrison Charter School was closed by the Texas Education Agency; the school was the first school of its kind to have its charter revoked in Texas.[3]

Rock guitarist and outdoorsman Ted Nugent, who is an enthusiastic bowhunter, resides in the Waco area. He filmed his MTV show Surviving Nugent on his ranch in nearby China Spring.

During the Presidency of George W. Bush, Waco was the home to the White House Press Center. The press center provided briefing and office facilities for the press corps whenever Bush visited his "Western White House" near Crawford. The former president's ranch is about west of Waco.